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| Open AccessChromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis
Ophiorrhiza pumila is a medicinal plant that can produce the anti-cancer monoterpene indole alkaloid (MIA) camptothecin. Here, the authors report its genome assembly and propose a working model for MIA evolution and biosynthesis through comparative genomics, synteny, and metabolic gene cluster analyses.
- Amit Rai
- , Hideki Hirakawa
- & Mami Yamazaki
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Article
| Open AccessDocking of acetyl-CoA carboxylase to the plastid envelope membrane attenuates fatty acid production in plants
In plants, light-dependent activation fatty acid synthesis (FAS) is mediated in part by acetyl-CoA carboxylase (ACCase). Here the authors identify a family of genes encoding carboxyltransferase interactors that attenuate FAS in the light by docking acetyl-CoA carboxylase to the plastid envelope.
- Yajin Ye
- , Krisztina Nikovics
- & Jay J. Thelen
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| Open AccessGenome-enabled discovery of anthraquinone biosynthesis in Senna tora
Anthraquinones are aromatic polyketides and have been used for treating various diseases, but the biosynthetic pathway is unclear. Here, the authors assemble the genome of an anthraquinone-producing medicinal plant Senna tora and show the evidences that CHS-like genes may be involved in anthraquinone biosynthesis.
- Sang-Ho Kang
- , Ramesh Prasad Pandey
- & Jae Kyung Sohng
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| Open AccessA cellulose synthase-derived enzyme catalyses 3-O-glucuronosylation in saponin biosynthesis
Saponins such as glycyrrhizin, a natural sweetener found in licorice root, are a class of triterpenoids synthesized that are characterized by a glucoronic acid moiety at the C-3 position. Here the authors show that saponin glucuronosylation is catalyzed by cellulose-synthase like enzymes and reconstitute glycyrrhizin synthesisin yeast.
- Soo Yeon Chung
- , Hikaru Seki
- & Toshiya Muranaka
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Article
| Open AccessMetabolite signatures of diverse Camellia sinensis tea populations
The molecular basis for the unique taste and aroma of tea cultivars is largely unknown, but is critical for breeding new cultivars. Here the authors use transcriptomics and metabolomics to study the relationship among phylogenetic groups and specialized metabolites from 136 tea accessions in China.
- Xiaomin Yu
- , Jiajing Xiao
- & Renyi Liu
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Article
| Open AccessFormation and diversification of a paradigm biosynthetic gene cluster in plants
How plant biosynthetic gene clusters (BGCs) form and evolve remains unclear. Here, via examining available genomes within and between Arabidopsis species, the authors show that the thalianol BGC has evolved recently and is still dynamically evolving through involvement of auxiliary genes and chromosomal inversions.
- Zhenhua Liu
- , Jitender Cheema
- & Anne Osbourn
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Article
| Open AccessUDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice
Increasing grain yield needs to be put in the context of environmental stress. Here, the authors reveal that a UDP-glucosyltransferase is associated with regulation of rice grain size, abiotic stress tolerance, flavonoid-mediated auxin signaling, and redirection of carbon flux to flavonoid glycosides synthesis.
- Nai-Qian Dong
- , Yuwei Sun
- & Hong-Xuan Lin
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Article
| Open AccessSynergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism
TRANSPARENT TESTA19 (TT19) encodes a glutathione S-transferase which functions in anthocyanin stabilization and vacuolar transport. Here, by tt19 suppressor screening, the authors show that RDR6/SGS3/DCL4 siRNA pathway constituents synergistically interact with components of the flavonoid pathway to control carbon metabolism.
- Nan Jiang
- , Aimer Gutierrez-Diaz
- & Erich Grotewold
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Article
| Open AccessIntegrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth
An increase in genomic selection (GS) accuracy can accelerate genetic gain by shortening the breeding cycles. Here, the authors introduce a network-based GS method that uses metabolic models and improves the prediction accuracy of Arabidopsis growth within and across environments.
- Hao Tong
- , Anika Küken
- & Zoran Nikoloski
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Article
| Open AccessThe chloroalkaloid (−)-acutumine is biosynthesized via a Fe(II)- and 2-oxoglutarate-dependent halogenase in Menispermaceae plants
Halogenated plant natural products are rare and plant halogenation enzymes are thus far unknown. Here Kim et al. identify a dechloroacutumine halogenase from Common Moonseed that catalyzes the final chlorination step in the biosynthesis of acutumine, a chloroalkaloid with selective cytotoxicity to cultured T cells.
- Colin Y. Kim
- , Andrew J. Mitchell
- & Jing-Ke Weng
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Article
| Open AccessA fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition
The fungal plant pathogen Zymoseptoria tritici is a major threat to wheat yield. Here Seybold et al. show that Z. tritici can suppress immune responses not only in infected tissue but also on other leaves, a phenomenon termed “systemic induced susceptibility” that is correlated with systemic changes in metabolite accumulation.
- Heike Seybold
- , Tobias J. Demetrowitsch
- & Eva H. Stukenbrock
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Article
| Open AccessIdentification and characterization of N9-methyltransferase involved in converting caffeine into non-stimulatory theacrine in tea
Kucha is a rare variety of tea tree that produces the non-stimulatory theacrine instead of caffeine. Here the authors show that theacrine synthase from Kucha has N9-methyltransferase activity resulting from amino acid substitutions that explain substrate specificity and could potentially guide production of caffeine-free tea.
- Yue-Hong Zhang
- , Yi-Fang Li
- & Rong-Rong He
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Article
| Open AccessGene clustering and copy number variation in alkaloid metabolic pathways of opium poppy
The opium poppy has been a source of painkilling drugs synthesized by the benzylisoquinoline alkaloid pathway. Here, the authors report an improved genome assembly and reveal gene clustering and copy number variation in alkaloid metabolic pathways.
- Qiushi Li
- , Sukanya Ramasamy
- & Sam Yeaman
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Article
| Open AccessGenome of Tripterygium wilfordii and identification of cytochrome P450 involved in triptolide biosynthesis
Tripterygium wilfordii is a medical plant that can produce antitumor activity compound triptolide. Here, the authors assemble its genome and identify a cytochrome P450 that can catalyze oxidation of a methyl to the acid moiety of dehydroabietic acid in triptolide biosynthesis by integrating multi-omics data.
- Lichan Tu
- , Ping Su
- & Wei Gao
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Article
| Open AccessPathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases
Steroidal glycoalkaloids (SGAs) accumulate in Solanum, but their hydroxylating enzymes are unknown. Here, the authors report 2-OXOGLUTARATE DEPENDENT DIOXYGENASE enzymes that catalyze the committed hydroxylation steps in the biosynthesis of leptinine insecticidal compounds in wild potato or non-bitter SGAs in cultivated tomato.
- Pablo D. Cárdenas
- , Prashant D. Sonawane
- & Asaph Aharoni
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| Open AccessChloroplastic metabolic engineering coupled with isoprenoid pool enhancement for committed taxanes biosynthesis in Nicotiana benthamiana
Engineering Taxol pathway in microbes needs to overcome the difficulty of expressing plant P450 enzymes. Here, the authors use a compartmentalized metabolic engineering strategy to construct the taxanes production pathway in chloroplasts of Nicotiana benthamiana and realize the production of taxadience-5α-ol.
- Jianhua Li
- , Ishmael Mutanda
- & Yong Wang
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Article
| Open AccessThe chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis
Black pepper (Piper nigrum) belongs to the long-isolated lineage of basal angiosperm and its fruit has been used for food spice and phytomedicines for thousands of years. Here, the authors assemble the reference genome of this species and analyze gene families associated with piperine biosynthesis.
- Lisong Hu
- , Zhongping Xu
- & Shuangxia Jin
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| Open AccessTropane alkaloids biosynthesis involves an unusual type III polyketide synthase and non-enzymatic condensation
Tropane alkaloids are medicinally significant plant metabolites generated by an unusual condensation of ornithine-derived and malonyl-CoA precursors. Here, Huang et al. show that pyrrolidine ketide synthase catalyzes a single round of condensation, which is followed by a non-enzymatic Mannich-like condensation.
- Jian-Ping Huang
- , Chengli Fang
- & Sheng-Xiong Huang
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| Open AccessEngineering a microbial biosynthesis platform for de novo production of tropane alkaloids
Tropane alkaloids (TAs) are a group of phytochemicals that are used to treat neurological disorders. Here, the authors engineer baker’s yeast to produce tropine, a key intermediate in the biosynthetic pathway of TAs, and cinnamoyltropine, a non-canonical TA, from simple carbon and nitrogen sources.
- Prashanth Srinivasan
- & Christina D. Smolke
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| Open AccessExpansion of a core regulon by transposable elements promotes Arabidopsis chemical diversity and pathogen defense
Arabidopsis plants can produce 4-hydroxyindole-3-carbonitrile (4OH-ICN) upon pathogen infection. Here, the authors show that EPCOT3, a retrotransposonderived enhancer, mediates WRKY33-binding, pathogen-responsive transcription of CYP82C2, and synthesis of 4OH-ICN.
- Brenden Barco
- , Yoseph Kim
- & Nicole K. Clay
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Article
| Open AccessEngineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria
The root microbiota is critical for promoting crop yield. Here, the authors create a synthetic pathway for the production of the rhizopine scyllo-inosamine in Medicago truncatula and barley, and show its perception by rhizosphere bacteria for targeted regulation of bacterial gene expression.
- Barney A. Geddes
- , Ponraj Paramasivan
- & Philip S. Poole
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| Open Access4-Coumarate 3-hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase
Lignin biosynthesis in higher plants relies upon a 3-hydroxylation reaction that can occur via shikimate esters of 4-coumarate. Here, Barros et al. define an alternative biosynthetic pathway via cytosolic ascorbate peroxidase that can catalyze direct 3-hydroxylation of 4-coumarate.
- Jaime Barros
- , Luis Escamilla-Trevino
- & Richard A. Dixon
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Article
| Open AccessThe apocarotenoid metabolite zaxinone regulates growth and strigolactone biosynthesis in rice
Strigolactone and abscisic acid are carotenoid-derived plant hormones. Here the authors describe the identification of zaxinone, a further apocarotenoid metabolite, which down-regulates strigolactone content and is required for normal growth and development in rice.
- Jian You Wang
- , Imran Haider
- & Salim Al-Babili
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Article
| Open AccessTropinone synthesis via an atypical polyketide synthase and P450-mediated cyclization
Tropinone is an intermediate in the biosynthesis of tropane alkaloids. Here, the authors discovered the enzymes AbPYKS and AbCYP82M3, a non-canonical polyketide synthase and a cytochrome P450, that work sequentially to form tropinone from N-methyl-Δ1-pyrrolinium cation.
- Matthew A. Bedewitz
- , A. Daniel Jones
- & Cornelius S. Barry
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| Open AccessRoot exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota
Plants can modify soil microbiota through root exudation, but how this process influences plant health in turn is often unclear. Here, Hu et al. show that maize benzoxazinoids released into the soil modify root-associated microbiota and thereby increase leaf defenses of the next plant generation.
- Lingfei Hu
- , Christelle A. M. Robert
- & Matthias Erb
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| Open AccessImproving wood properties for wood utilization through multi-omics integration in lignin biosynthesis
A systematic analysis of lignin biosynthetic genes to quantitatively understand their effect on wood properties is still lacking. Here, the authors integrate transcriptomic, proteomic, fluxomic and phenomic data to quantify the impact of perturbations of transcript abundance on lignin biosynthesis and wood properties.
- Jack P. Wang
- , Megan L. Matthews
- & Vincent L. Chiang
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| Open AccessOxidative rearrangement of (+)-sesamin by CYP92B14 co-generates twin dietary lignans in sesame
Sesame seeds contain phenylpropanoid-derived lignans that are potentially beneficial to human health. Here, the authors clone a cytochrome P450 enzyme that is responsible for the last steps of sesame lignan biosynthesis and show that it acts through a novel oxidative rearrangement mechanism.
- Jun Murata
- , Eiichiro Ono
- & Manabu Horikawa
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| Open AccessEvolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity
Plants produce large numbers of structurally diverse metabolites through multistep pathways that often use the same precursors. Here the authors utilize the pathway leading to the production of acylated sucroses in the tomato plant to illustrate how metabolite diversity can arise through biochemical pathway evolution.
- Pengxiang Fan
- , Abigail M. Miller
- & Robert L. Last
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| Open AccessA phenol-enriched cuticle is ancestral to lignin evolution in land plants
The phenolic polymer lignin is thought to have contributed to adaptation of early land plants to terrestrial environments. Here Renaultet al. show that moss, which does not produce lignin, contains an ancestral phenolic metabolism pathway that produces a phenol-enriched cuticle and prevents desiccation.
- Hugues Renault
- , Annette Alber
- & Danièle Werck-Reichhart
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| Open AccessThe ancient CYP716 family is a major contributor to the diversification of eudicot triterpenoid biosynthesis
Cytochrome P450 family enzymes have an essential role in the creation of triterpenoid diversity in plants. Here, the authors describe triterpenoid synthesis as mediated by CYP716 enzymes in medicinal plant species, and perform phylogenetic analysis to describe CYP716 molecular evolution in plants.
- Karel Miettinen
- , Jacob Pollier
- & Alain Goossens
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| Open AccessEvolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism
Genes in the cytochrome P450 family have evolved a wide range of functions. Here, Liu et al. reconstruct the evolution of the P450 genes CYP98A8 and CYP98A9in the Brassicales, revealing a complex history of retrotransposition, tandem duplication and neofunctionalization, followed by subfunctionalization or gene loss in specific lineages.
- Zhenhua Liu
- , Raquel Tavares
- & Hugues Renault
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| Open AccessElucidation of the biosynthesis of carnosic acid and its reconstitution in yeast
Diterpenes are plant products with high antioxidant properties and potential application as food additives and therapeutics. Here, the authors describe the complete biosynthetic pathway of carnosic acid and reconstruct it in yeast, opening the way to metabolic engineering of phenolic diterpenes.
- Ulschan Scheler
- , Wolfgang Brandt
- & Alain Tissier
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| Open AccessCharacterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae
Protection from UV-B is critical for land plant survival. Here Tohge et al. show that saiginols, a novel class of flavonols that efficiently absorb UV-B, accumulate in Arabidopsisaccessions collected from high irradiance regions and identify a flavonol phenylacyltransferase gene required for saiginol production.
- Takayuki Tohge
- , Regina Wendenburg
- & Alisdair R. Fernie
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| Open AccessStructural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity
The stereochemistry of the plant heteroyohimbine alkaloids is a key factor determining their diverse biological activities. Here, the authors carry out structural, localization and genetic experiments to understand the mechanism of stereoselectivity for three heteroyohimbine synthases and to identify their function in vivo.
- Anna Stavrinides
- , Evangelos C. Tatsis
- & Sarah E. O'Connor
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An alternative pathway contributes to phenylalanine biosynthesis in plants via a cytosolic tyrosine:phenylpyruvate aminotransferase
Plants primarily synthesize phenylalanine in plastids via arogenate. Here, Yoo et al. provide evidence that petunia flowers also employ an alternative microbial-like pathway to synthesize phenylalanine that is partially localized in the cytosol and interconnected with tyrosine catabolism.
- Heejin Yoo
- , Joshua R. Widhalm
- & Natalia Dudareva
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| Open AccessA bacterial platform for fermentative production of plant alkaloids
Secondary metabolites are widely used in human health and nutrition, but extraction yields from plants are often low. Nakagawaet al. have engineered the metabolism of Escherichia colito develop a fermentation system that produces plant alkaloids from simple carbon sources.
- Akira Nakagawa
- , Hiromichi Minami
- & Hidehiko Kumagai
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Two splice variants of the IDD14 transcription factor competitively form nonfunctional heterodimers which may regulate starch metabolism
The alternative splicing of genes increases the number and diversity of proteins produced within a cell. Seoet al. demonstrate that the beta form of the alternatively spliced Arabidopsis gene, IDD14, is produced under cold conditions and may have a role in regulating starch accumulation.
- Pil Joon Seo
- , Mi Jung Kim
- & Chung-Mo Park